FMO DATABASE

FMODB ID: YZ862

Calculation Name: 4H32-F-Xray372

Preferred Name:

Target Type:

Ligand Name: 2-acetamido-2-deoxy-beta-d-glucopyranose

ligand 3-letter code: NAG

PDB ID: 4H32

Chain ID: F

ChEMBL ID:

UniProt ID: H6QM93

Base Structure: X-ray

Registration Date: 2023-09-19

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	170
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1452615.121968
FMO2-HF: Nuclear repulsion	1382669.818167
FMO2-HF: Total energy	-69945.303801
FMO2-MP2: Total energy	-70146.888757

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(F:335:ALA)

Summations of interaction energy for fragment #1(F:335:ALA)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-14.191	-9.591	2.911	-3.087	-4.424	0.01

Interaction energy analysis for fragmet #1(F:335:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.014 / q_NPA : -0.019

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	F	337	PHE	0	-0.066	-0.041	3.792	-2.287	-0.675	-0.028	-0.726	-0.858	-0.001
4	F	338	ILE	0	0.036	0.056	5.713	-0.217	-0.217	0.000	0.000	0.000	0.000
5	F	339	GLU	-1	-0.924	-0.965	8.769	-0.009	-0.009	0.000	0.000	0.000	0.000
6	F	340	GLY	0	-0.012	-0.018	7.918	-0.220	-0.220	0.000	0.000	0.000	0.000
7	F	341	GLY	0	-0.019	-0.006	7.964	0.252	0.252	0.000	0.000	0.000	0.000
8	F	342	TRP	0	-0.005	-0.019	3.135	-0.136	0.677	0.093	-0.298	-0.608	0.000
9	F	343	GLN	0	0.006	0.003	6.277	-0.015	-0.015	0.000	0.000	0.000	0.000
10	F	344	GLY	0	-0.020	-0.015	7.210	-0.110	-0.110	0.000	0.000	0.000	0.000
11	F	345	MET	0	-0.043	0.014	8.154	0.269	0.269	0.000	0.000	0.000	0.000
12	F	346	ILE	0	-0.013	-0.020	9.022	-0.101	-0.101	0.000	0.000	0.000	0.000
13	F	347	ASP	-1	-0.896	-0.950	12.711	0.528	0.528	0.000	0.000	0.000	0.000
14	F	348	GLY	0	-0.059	-0.045	14.333	-0.040	-0.040	0.000	0.000	0.000	0.000
15	F	349	TRP	0	-0.025	-0.001	13.728	0.040	0.040	0.000	0.000	0.000	0.000
16	F	350	TYR	0	0.027	-0.044	12.642	0.063	0.063	0.000	0.000	0.000	0.000
17	F	351	GLY	0	0.019	0.000	11.002	-0.109	-0.109	0.000	0.000	0.000	0.000
18	F	352	TYR	0	-0.074	-0.049	9.146	0.080	0.080	0.000	0.000	0.000	0.000
19	F	353	HIS	0	-0.019	-0.019	2.362	-8.316	-7.463	2.760	-1.498	-2.115	0.013
20	F	354	HIS	0	0.001	0.011	6.611	-0.076	-0.076	0.000	0.000	0.000	0.000
21	F	355	GLU	-1	-0.902	-0.961	3.904	-1.676	-1.278	0.001	-0.151	-0.249	-0.001
22	F	356	ASN	0	-0.058	-0.049	7.832	-0.090	-0.090	0.000	0.000	0.000	0.000
23	F	357	GLN	0	-0.069	-0.041	11.460	-0.057	-0.057	0.000	0.000	0.000	0.000
24	F	358	GLU	-1	-0.871	-0.948	14.413	0.122	0.122	0.000	0.000	0.000	0.000
25	F	359	GLY	0	-0.015	0.005	11.220	-0.022	-0.022	0.000	0.000	0.000	0.000
26	F	360	SER	0	0.016	0.009	6.135	-0.054	-0.054	0.000	0.000	0.000	0.000
27	F	361	GLY	0	-0.016	-0.012	7.275	-0.195	-0.195	0.000	0.000	0.000	0.000
28	F	362	TYR	0	0.030	0.016	2.687	-1.086	-0.162	0.085	-0.414	-0.594	-0.001
29	F	363	ALA	0	-0.015	-0.020	8.175	-0.373	-0.373	0.000	0.000	0.000	0.000
30	F	364	ALA	0	0.055	0.039	11.562	0.116	0.116	0.000	0.000	0.000	0.000
31	F	365	ASP	-1	-0.806	-0.899	13.426	0.396	0.396	0.000	0.000	0.000	0.000
32	F	366	LYS	1	0.975	0.962	16.039	-0.411	-0.411	0.000	0.000	0.000	0.000
33	F	367	GLU	-1	-0.959	-0.964	18.921	0.260	0.260	0.000	0.000	0.000	0.000
34	F	368	ALA	0	0.031	0.017	18.120	-0.033	-0.033	0.000	0.000	0.000	0.000
35	F	369	THR	0	-0.016	-0.008	16.772	-0.003	-0.003	0.000	0.000	0.000	0.000
36	F	370	GLN	0	-0.009	-0.012	19.138	-0.013	-0.013	0.000	0.000	0.000	0.000
37	F	371	LYS	1	0.949	0.987	22.618	-0.243	-0.243	0.000	0.000	0.000	0.000
38	F	372	ALA	0	0.026	0.017	20.508	-0.024	-0.024	0.000	0.000	0.000	0.000
39	F	373	VAL	0	0.005	0.001	21.027	-0.022	-0.022	0.000	0.000	0.000	0.000
40	F	374	ASP	-1	-0.892	-0.938	23.515	0.160	0.160	0.000	0.000	0.000	0.000
41	F	375	ALA	0	-0.036	-0.023	25.549	-0.017	-0.017	0.000	0.000	0.000	0.000
42	F	376	ILE	0	-0.007	-0.007	22.967	-0.015	-0.015	0.000	0.000	0.000	0.000
43	F	377	THR	0	-0.012	-0.008	26.200	-0.016	-0.016	0.000	0.000	0.000	0.000
44	F	378	ASN	0	-0.057	-0.032	28.458	-0.016	-0.016	0.000	0.000	0.000	0.000
45	F	379	LYS	1	0.889	0.952	26.890	-0.130	-0.130	0.000	0.000	0.000	0.000
46	F	380	VAL	0	0.008	-0.001	28.012	-0.010	-0.010	0.000	0.000	0.000	0.000
47	F	381	ASN	0	0.038	0.007	30.940	-0.007	-0.007	0.000	0.000	0.000	0.000
48	F	382	SER	0	-0.074	-0.015	33.745	-0.009	-0.009	0.000	0.000	0.000	0.000
49	F	383	ILE	0	-0.042	-0.030	31.857	-0.006	-0.006	0.000	0.000	0.000	0.000
50	F	384	ILE	0	-0.029	-0.003	33.187	-0.005	-0.005	0.000	0.000	0.000	0.000
51	F	385	ASP	-1	-0.891	-0.956	36.827	0.075	0.075	0.000	0.000	0.000	0.000
52	F	386	LYS	1	0.824	0.916	39.018	-0.071	-0.071	0.000	0.000	0.000	0.000
53	F	387	MET	0	-0.018	0.014	40.999	-0.004	-0.004	0.000	0.000	0.000	0.000
54	F	388	ASN	0	-0.021	-0.024	42.729	0.001	0.001	0.000	0.000	0.000	0.000
55	F	389	SER	0	-0.012	-0.007	45.943	-0.001	-0.001	0.000	0.000	0.000	0.000
56	F	390	GLN	0	0.009	0.006	48.153	0.001	0.001	0.000	0.000	0.000	0.000
57	F	391	PHE	0	-0.018	-0.002	51.548	0.000	0.000	0.000	0.000	0.000	0.000
58	F	392	GLU	-1	-0.950	-0.974	52.001	0.028	0.028	0.000	0.000	0.000	0.000
59	F	393	SER	0	-0.056	-0.029	54.493	0.000	0.000	0.000	0.000	0.000	0.000
60	F	394	ASN	0	0.036	0.019	53.794	0.000	0.000	0.000	0.000	0.000	0.000
61	F	395	ILE	0	-0.009	-0.009	56.750	0.000	0.000	0.000	0.000	0.000	0.000
62	F	396	LYS	1	1.015	1.001	56.706	-0.016	-0.016	0.000	0.000	0.000	0.000
63	F	397	GLU	-1	-1.042	-1.001	60.131	0.015	0.015	0.000	0.000	0.000	0.000
64	F	398	PHE	0	0.029	0.007	62.742	0.000	0.000	0.000	0.000	0.000	0.000
65	F	399	ASN	0	-0.099	-0.032	65.906	-0.001	-0.001	0.000	0.000	0.000	0.000
66	F	400	ARG	1	0.992	0.989	68.010	-0.009	-0.009	0.000	0.000	0.000	0.000
67	F	401	LEU	0	0.043	0.007	70.147	0.000	0.000	0.000	0.000	0.000	0.000
68	F	402	GLU	-1	-0.754	-0.877	67.916	0.013	0.013	0.000	0.000	0.000	0.000
69	F	403	LEU	0	-0.038	-0.029	67.438	0.000	0.000	0.000	0.000	0.000	0.000
70	F	404	ARG	1	0.894	0.965	64.986	-0.013	-0.013	0.000	0.000	0.000	0.000
71	F	405	ILE	0	0.020	-0.018	64.883	0.000	0.000	0.000	0.000	0.000	0.000
72	F	406	GLN	0	0.048	0.022	61.878	0.001	0.001	0.000	0.000	0.000	0.000
73	F	407	HIS	0	-0.016	0.005	61.203	0.000	0.000	0.000	0.000	0.000	0.000
74	F	408	LEU	0	-0.076	-0.042	60.706	0.000	0.000	0.000	0.000	0.000	0.000
75	F	409	SER	0	0.042	0.012	59.085	0.001	0.001	0.000	0.000	0.000	0.000
76	F	410	ASP	-1	-0.843	-0.908	57.378	0.016	0.016	0.000	0.000	0.000	0.000
77	F	411	ARG	1	0.899	0.944	56.119	-0.016	-0.016	0.000	0.000	0.000	0.000
78	F	412	VAL	0	-0.048	-0.027	55.319	0.001	0.001	0.000	0.000	0.000	0.000
79	F	413	ASP	-1	-0.870	-0.926	53.315	0.022	0.022	0.000	0.000	0.000	0.000
80	F	414	ASP	-1	-0.906	-0.957	51.518	0.018	0.018	0.000	0.000	0.000	0.000
81	F	415	ALA	0	-0.064	-0.029	50.588	0.001	0.001	0.000	0.000	0.000	0.000
82	F	416	LEU	0	-0.011	-0.024	49.810	0.001	0.001	0.000	0.000	0.000	0.000
83	F	417	LEU	0	-0.013	0.009	45.672	0.002	0.002	0.000	0.000	0.000	0.000
84	F	418	ASP	-1	-0.881	-0.943	45.780	0.021	0.021	0.000	0.000	0.000	0.000
85	F	419	ILE	0	-0.072	-0.036	45.122	0.001	0.001	0.000	0.000	0.000	0.000
86	F	420	TRP	0	0.012	-0.002	42.240	0.003	0.003	0.000	0.000	0.000	0.000
87	F	421	SER	0	-0.022	0.016	41.488	0.003	0.003	0.000	0.000	0.000	0.000
88	F	422	TYR	0	-0.005	0.003	40.119	0.001	0.001	0.000	0.000	0.000	0.000
89	F	423	ASN	0	0.004	-0.014	39.592	0.000	0.000	0.000	0.000	0.000	0.000
90	F	424	THR	0	-0.036	-0.045	36.603	0.004	0.004	0.000	0.000	0.000	0.000
91	F	425	GLU	-1	-0.933	-0.957	35.460	0.039	0.039	0.000	0.000	0.000	0.000
92	F	426	LEU	0	-0.019	-0.011	34.390	0.003	0.003	0.000	0.000	0.000	0.000
93	F	427	LEU	0	-0.014	0.005	34.113	0.004	0.004	0.000	0.000	0.000	0.000
94	F	428	VAL	0	0.003	-0.006	30.358	0.007	0.007	0.000	0.000	0.000	0.000
95	F	429	LEU	0	-0.042	-0.022	29.924	0.006	0.006	0.000	0.000	0.000	0.000
96	F	430	LEU	0	0.021	0.020	29.271	0.004	0.004	0.000	0.000	0.000	0.000
97	F	431	GLU	-1	-0.861	-0.955	29.146	0.099	0.099	0.000	0.000	0.000	0.000
98	F	432	ASN	0	-0.028	-0.007	25.662	0.020	0.020	0.000	0.000	0.000	0.000
99	F	433	GLU	-1	-0.920	-0.947	24.468	0.072	0.072	0.000	0.000	0.000	0.000
100	F	434	ARG	1	0.952	0.975	24.574	-0.086	-0.086	0.000	0.000	0.000	0.000
101	F	435	THR	0	-0.064	-0.045	22.303	0.015	0.015	0.000	0.000	0.000	0.000
102	F	436	LEU	0	-0.026	-0.018	19.701	0.026	0.026	0.000	0.000	0.000	0.000
103	F	437	ASP	-1	-0.835	-0.906	19.789	0.128	0.128	0.000	0.000	0.000	0.000
104	F	438	PHE	0	-0.127	-0.060	21.542	0.016	0.016	0.000	0.000	0.000	0.000
105	F	439	HIS	0	0.015	0.050	17.052	0.046	0.046	0.000	0.000	0.000	0.000
106	F	440	ASP	-1	-0.853	-0.910	16.536	0.263	0.263	0.000	0.000	0.000	0.000
107	F	441	ALA	0	-0.036	-0.028	17.404	0.025	0.025	0.000	0.000	0.000	0.000
108	F	442	ASN	0	-0.053	-0.036	18.255	-0.008	-0.008	0.000	0.000	0.000	0.000
109	F	443	VAL	0	0.008	0.002	12.984	0.038	0.038	0.000	0.000	0.000	0.000
110	F	444	LYS	1	0.965	0.997	14.729	-0.132	-0.132	0.000	0.000	0.000	0.000
111	F	445	ASN	0	-0.013	-0.021	16.892	-0.026	-0.026	0.000	0.000	0.000	0.000
112	F	446	LEU	0	-0.042	-0.011	13.374	-0.026	-0.026	0.000	0.000	0.000	0.000
113	F	447	PHE	0	0.007	0.018	12.676	0.018	0.018	0.000	0.000	0.000	0.000
114	F	448	GLU	-1	-0.900	-0.968	15.291	0.144	0.144	0.000	0.000	0.000	0.000
115	F	449	LYS	1	0.934	0.964	18.740	-0.337	-0.337	0.000	0.000	0.000	0.000
116	F	450	VAL	0	-0.017	0.004	14.037	-0.031	-0.031	0.000	0.000	0.000	0.000
117	F	451	LYS	1	0.968	0.999	17.202	-0.142	-0.142	0.000	0.000	0.000	0.000
118	F	452	ALA	0	-0.035	-0.010	18.421	-0.034	-0.034	0.000	0.000	0.000	0.000
119	F	453	GLN	0	-0.062	-0.014	18.982	-0.043	-0.043	0.000	0.000	0.000	0.000
120	F	454	LEU	0	0.021	0.012	14.974	-0.026	-0.026	0.000	0.000	0.000	0.000
121	F	455	LYS	1	0.829	0.906	19.532	-0.154	-0.154	0.000	0.000	0.000	0.000
122	F	456	ASP	-1	-0.832	-0.857	20.144	0.048	0.048	0.000	0.000	0.000	0.000
123	F	457	ASN	0	0.001	0.005	20.331	-0.034	-0.034	0.000	0.000	0.000	0.000
124	F	458	ALA	0	0.007	0.000	15.267	0.005	0.005	0.000	0.000	0.000	0.000
125	F	459	ILE	0	-0.020	-0.011	15.370	0.002	0.002	0.000	0.000	0.000	0.000
126	F	460	ASP	-1	-0.877	-0.941	14.001	0.060	0.060	0.000	0.000	0.000	0.000
127	F	461	GLU	-1	-0.921	-0.968	8.926	-0.628	-0.628	0.000	0.000	0.000	0.000
128	F	462	GLY	0	-0.069	-0.029	12.673	-0.077	-0.077	0.000	0.000	0.000	0.000
129	F	463	ASN	0	0.023	0.001	7.327	0.250	0.250	0.000	0.000	0.000	0.000
130	F	464	GLY	0	0.036	0.010	8.750	0.081	0.081	0.000	0.000	0.000	0.000
131	F	465	CYS	0	-0.058	-0.003	6.685	0.376	0.376	0.000	0.000	0.000	0.000
132	F	466	PHE	0	-0.012	-0.022	9.429	-0.135	-0.135	0.000	0.000	0.000	0.000
133	F	467	LEU	0	0.047	0.031	11.172	0.049	0.049	0.000	0.000	0.000	0.000
134	F	468	LEU	0	-0.006	-0.010	12.346	0.020	0.020	0.000	0.000	0.000	0.000
135	F	469	LEU	0	-0.052	-0.016	14.798	-0.038	-0.038	0.000	0.000	0.000	0.000
136	F	470	HIS	0	0.066	0.028	17.179	0.008	0.008	0.000	0.000	0.000	0.000
137	F	471	LYS	1	0.922	0.971	16.113	0.036	0.036	0.000	0.000	0.000	0.000
138	F	472	CYS	0	0.010	0.030	14.330	0.031	0.031	0.000	0.000	0.000	0.000
139	F	473	ASN	0	0.067	0.048	14.815	0.038	0.038	0.000	0.000	0.000	0.000
140	F	474	ASN	0	0.053	0.004	14.389	0.050	0.050	0.000	0.000	0.000	0.000
141	F	475	SER	0	-0.017	0.006	16.297	0.030	0.030	0.000	0.000	0.000	0.000
142	F	477	MET	0	0.004	-0.009	10.805	0.046	0.046	0.000	0.000	0.000	0.000
143	F	478	ASP	-1	-0.912	-0.967	15.175	0.456	0.456	0.000	0.000	0.000	0.000
144	F	479	ASP	-1	-0.920	-0.956	17.575	0.208	0.208	0.000	0.000	0.000	0.000
145	F	480	ILE	0	-0.029	-0.013	14.895	-0.013	-0.013	0.000	0.000	0.000	0.000
146	F	481	LYS	1	0.857	0.938	11.254	-0.874	-0.874	0.000	0.000	0.000	0.000
147	F	482	ASN	0	-0.066	-0.018	16.590	-0.004	-0.004	0.000	0.000	0.000	0.000
148	F	483	GLY	0	-0.059	-0.021	19.650	-0.036	-0.036	0.000	0.000	0.000	0.000
149	F	484	THR	0	-0.037	-0.032	21.460	-0.023	-0.023	0.000	0.000	0.000	0.000
150	F	485	TYR	0	-0.004	0.005	19.204	-0.026	-0.026	0.000	0.000	0.000	0.000
151	F	486	LYS	1	0.941	0.967	21.788	-0.128	-0.128	0.000	0.000	0.000	0.000
152	F	487	TYR	0	-0.066	-0.107	23.344	-0.005	-0.005	0.000	0.000	0.000	0.000
153	F	488	MET	0	-0.006	-0.029	24.695	-0.008	-0.008	0.000	0.000	0.000	0.000
154	F	489	ASP	-1	-0.933	-0.950	25.120	0.088	0.088	0.000	0.000	0.000	0.000
155	F	490	TYR	0	0.024	0.014	21.367	0.000	0.000	0.000	0.000	0.000	0.000
156	F	491	ARG	1	0.865	0.938	23.571	-0.049	-0.049	0.000	0.000	0.000	0.000
157	F	492	GLU	-1	-0.931	-0.973	25.655	0.013	0.013	0.000	0.000	0.000	0.000
158	F	493	GLU	-1	-0.896	-0.961	21.718	0.026	0.026	0.000	0.000	0.000	0.000
159	F	494	SER	0	0.021	0.016	21.251	-0.008	-0.008	0.000	0.000	0.000	0.000
160	F	495	HIS	0	-0.111	-0.064	22.684	-0.010	-0.010	0.000	0.000	0.000	0.000
161	F	496	ILE	0	-0.031	-0.005	25.715	-0.010	-0.010	0.000	0.000	0.000	0.000
162	F	497	GLU	-1	-0.933	-0.966	19.425	-0.091	-0.091	0.000	0.000	0.000	0.000
163	F	498	LYS	1	0.941	0.971	22.301	0.013	0.013	0.000	0.000	0.000	0.000
164	F	499	GLN	0	0.019	0.010	23.197	-0.002	-0.002	0.000	0.000	0.000	0.000
165	F	500	LYS	1	0.937	0.967	23.146	0.066	0.066	0.000	0.000	0.000	0.000
166	F	501	ILE	0	-0.039	-0.010	18.946	-0.010	-0.010	0.000	0.000	0.000	0.000
167	F	502	ASP	-1	-0.945	-0.972	23.094	-0.068	-0.068	0.000	0.000	0.000	0.000
168	F	503	GLY	0	-0.033	0.001	26.191	0.003	0.003	0.000	0.000	0.000	0.000
169	F	504	VAL	0	-0.018	-0.018	28.095	0.008	0.008	0.000	0.000	0.000	0.000
170	F	505	GLU	-1	-1.029	-1.006	30.637	-0.068	-0.068	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(F:335:ALA)